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## S

s_mrkIdxL - Variable in class org.metaqtl.Qtl.QTLProj
  The skeleton indice of the left flanking marker.
s_mrkIdxR - Variable in class org.metaqtl.Qtl.QTLProj
  The skeleton indice of the right flanking marker.
scale(double) - Method in class org.metaqtl.graph.ChromAxe
  Scale the axe in y.
scaleHeight(double) - Method in class org.metaqtl.graph.ChromAxe
scaleY(double) - Method in class org.metaqtl.graph.ChromAxe
sd - Variable in class org.metaqtl.MetaQtlResult
  The QTL position standard deviations.
sd2ci(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
sd_mode - Variable in class org.metaqtl.algo.QtlProjAlgorithm
  The mode of compuation of the standard deviation of the QTL positions.
sd_position - Variable in class org.metaqtl.Qtl
  The standard deviation of the QTL position.
sdd - Variable in class org.metaqtl.MetaChrom
  The standard deviation of the position in Morgan.
selfingIndividualInformation(OffspringManager.HaldaneWaddingtonProportion) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the individual means amount of information for the given generation propertions for a self-fertilization design.
selfingRecurrence(OffspringManager.HaldaneWaddingtonProportion, double) - Static method in class org.metaqtl.util.OffspringManager
  Given the current proportion C,D,E,F and G and the recombination rate r this routine computes the next generation proportions following the recurrence formula of Haldane and Waddington, 1931, Inbreeding and linkage, Genetics 16:357-374 (see section self-fertilization p358).
SEPARATOR - Static variable in class org.metaqtl.factory.MetaQtlModelFactory
set(String, String) - Static method in class org.metaqtl.graph.MetaGraphPar
setCentroid(double) - Method in class org.metaqtl.TreeNode
setChildren(OntologyTerm[]) - Method in class org.thalia.bio.entity.OntologyTerm
  Sets the children of the term.
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlPartitionLayer
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlTreeLayer
setChromName(int, String) - Method in class org.metaqtl.MetaQtlModel
setCIMiss(int) - Method in class org.metaqtl.algo.ClustAlgorithm
setCIMode(int) - Method in class org.metaqtl.algo.ClustAlgorithm
setClusterings(List) - Method in class org.metaqtl.MetaQtlResult
setClusterings(EMResult[]) - Method in class org.metaqtl.MetaQtlResult
setCriterion(String) - Method in class org.metaqtl.MetaQtlModel
  Set the criterion name which was used to obtain this model
setCrossDesign(IBioGenome, CrossPopulation) - Static method in class org.metaqtl.util.GeneticMapProperties
setCrossType(int) - Method in class org.thalia.bio.entity.CrossPopulation
setDF(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
  Sets the derivative of the function at x.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.ChromCluster
  This method sets the list of dubious marker.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.MapCluster
  This method sets the list of dubious marker.
setEMEps(double) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setEMRanStartNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setFunction(String) - Method in class org.thalia.bio.entity.Ontology
  Set the function of the ontology.
setGeneration(int) - Method in class org.thalia.bio.entity.Population
setGenome(IBioGenome) - Method in class org.thalia.bio.entity.LocusContainer
setGenome(IBioGenome) - Method in interface org.thalia.bio.IBioLGroup
setGroup(IBioLGroup) - Method in class org.thalia.bio.entity.AlleleContainer
setGroup(IBioLGroup) - Method in class org.thalia.bio.entity.Locus
setGroup(IBioLGroup) - Method in interface org.thalia.bio.IBioLocus
setGroups(ArrayList) - Method in class org.thalia.bio.entity.bean.GeneticMapBean
setID(long) - Method in class org.thalia.bio.entity.OntologyTerm
  Sets the indentifient of the term.
setIgnore(boolean) - Method in class org.metaqtl.Qtl
  Set the status of the QTL.
setLabelSide(int) - Method in class org.metaqtl.graph.ChromLayer
setLabelSide(int) - Method in class org.metaqtl.graph.ChromShape
setLoci(IBioLocus[]) - Method in class org.thalia.bio.entity.LocusContainer
setLoci(IBioLocus[]) - Method in interface org.thalia.bio.IBioLGroup
setLocus(ArrayList) - Method in class org.thalia.bio.entity.bean.LGroupBean
setLocus(IBioLocus) - Method in interface org.thalia.bio.IBioAllele
setLogger(Writer) - Method in class org.metaqtl.algo.MetaAlgorithm
setLogger(OutputStream) - Method in class org.metaqtl.algo.MetaAlgorithm
setLogger(Writer) - Method in interface org.metaqtl.IMetaAlgorithm
  Give a `Writer` to the algorithm in order to write out the log info.
setLogger(OutputStream) - Method in interface org.metaqtl.IMetaAlgorithm
  Give a `OutputStream` to the algorithm in order to write out the log info.
setMappingContext(IBioGenome, int, int) - Static method in class org.metaqtl.util.GeneticMapProperties
setMarkerDico(MetaDico) - Method in class org.metaqtl.algo.MetaMapAlgorithm
setMarkerDico(MetaDico) - Method in class org.metaqtl.ChromCluster
setMarkerDico(MetaDico) - Method in class org.metaqtl.MapCluster
setMaxClusterNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setMetaQtls(Qtl[]) - Method in class org.metaqtl.Chromosome
setModel(int, int[]) - Method in class org.metaqtl.MetaQtlModel
setMrkThresh(int) - Method in class org.metaqtl.ChromCluster
setMrkThreshold(int) - Method in class org.metaqtl.algo.MetaMapAlgorithm
setName(String) - Method in class org.thalia.bio.entity.bean.BioEntityBean
setName(String) - Method in class org.thalia.bio.entity.bean.PropertyBean
setName(String) - Method in class org.thalia.bio.entity.BioEntity
setName(String) - Method in class org.thalia.bio.entity.BioEntityCollection
setName(String) - Method in interface org.thalia.bio.IBioEntity
setParameter(String) - Static method in class org.metaqtl.main.MetaMain
setParentTerm(IBioOntologyTerm) - Method in class org.thalia.bio.entity.OntologyTerm
  Sets the parent of the term.
setPedigree(IBioIndividualTree) - Method in class org.thalia.bio.entity.Individual
setPopulation(IBioPopulation) - Method in class org.thalia.bio.entity.Individual
setPopulation(IBioPopulation) - Method in interface org.thalia.bio.IBioIndividual
setPosition(ILGroupPosition) - Method in class org.thalia.bio.entity.AlleleContainer
setPosition(ILGroupPosition) - Method in class org.thalia.bio.entity.Locus
setPosition(double) - Method in class org.thalia.bio.entity.Locus
  Set the position of the locus on the linkage group in static mode i.e without uncertainty.
setPosition(double, double) - Method in class org.thalia.bio.entity.Locus
  Set the position of the locus on the linkage group in estimate mode i.e with uncertainty.
setPosition(ILGroupPosition) - Method in interface org.thalia.bio.IBioLocus
setPosition(double) - Method in interface org.thalia.bio.IBioLocus
setPosition(double, double) - Method in interface org.thalia.bio.IBioLocus
setProba(double[][]) - Method in class org.metaqtl.Chromosome
setProperties(ArrayList) - Method in class org.thalia.bio.entity.bean.BioEntityBean
setProperties(Properties) - Method in class org.thalia.bio.entity.BioEntity
setProperties(Properties) - Method in class org.thalia.bio.entity.BioEntityCollection
setProperties(Properties) - Method in interface org.thalia.bio.IBioEntity
  Sets the properties of the entity.
setPvalue(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
setQtlIdx(int[]) - Method in class org.metaqtl.MetaQtlResult
  Set the indices of the Qtl which are implied in this result.
setRatio(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
setRoot(IBioOntologyTerm) - Method in class org.thalia.bio.entity.Ontology
setRoot(OntologyTerm) - Method in class org.thalia.bio.entity.Ontology
setRoot(IBioOntologyTerm) - Method in interface org.thalia.bio.IBioOntology
  Sets the root of the ontology.
setSD(Double[]) - Method in class org.metaqtl.MetaQtlResult
  Set the standard deviations of the Qtl.
setSize(int) - Method in class org.thalia.bio.entity.Population
  Set the population size.
setTerm(String, List) - Method in class org.metaqtl.MetaDico
setTraitNames(int, String[]) - Method in class org.metaqtl.MetaQtlModel
setTree(Tree) - Method in class org.metaqtl.MetaQtlResult
setTree(Tree) - Method in class org.metaqtl.QtlPartition
setTreeMethod(int) - Method in class org.metaqtl.algo.QtlTreeAlgorithm
setValue(String) - Method in class org.thalia.bio.entity.bean.PropertyBean
setX(double) - Method in class org.metaqtl.graph.AnchoredElement
setX(double) - Method in class org.metaqtl.graph.ChromAxe
setX(Double[]) - Method in class org.metaqtl.MetaQtlResult
  Set the observed positions of the Qtl.
setX(double) - Method in class org.metaqtl.TreeNode
setY(double) - Method in class org.metaqtl.graph.AnchoredElement
setY(double) - Method in class org.metaqtl.TreeNode
setYMax(double) - Method in class org.metaqtl.graph.ChromAxe
setYMin(double) - Method in class org.metaqtl.graph.ChromAxe
SF - Static variable in interface org.thalia.bio.IBioCrossTypes
shareFlanking - Variable in class org.metaqtl.Qtl.QTLProj
  True if the two maps share a common marker sequence around the QTL.
shortForm() - Method in class org.metaqtl.main.CmdLineParser.Option
SIGN(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns abs(a) if b > 0, -abs(a) otherwise.
SINGLE_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
SINGLE_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
size - Variable in class org.metaqtl.Qtl.QTLCross
  The number of individuals.
skeleton - Variable in class org.metaqtl.Chromosome
  The skeleton status for this member
sortCluster() - Method in class org.metaqtl.EMResult
  Sort the components in increasing order.
sortLociByPosition(IBioLocus[]) - Static method in class org.thalia.bio.util.BioUtilities
  Sort tab with loci
SQR(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns a^2
standardError() - Method in interface org.thalia.bio.util.ILGroupPosition
standardError() - Method in class org.thalia.bio.util.LGroupPosition
STATIC - Static variable in interface org.thalia.bio.util.ILGroupPosition
StaticLocusPosition - Class in org.thalia.bio.util
  Class Description Here
StaticLocusPosition(double) - Constructor for class org.thalia.bio.util.StaticLocusPosition
stats - Variable in class org.metaqtl.Qtl
  The QTL statistics
stderr - Variable in class org.thalia.bio.entity.bean.LocusBean
string2color(String) - Static method in class org.metaqtl.graph.MetaGraphPar
string2font(String) - Static method in class org.metaqtl.graph.MetaGraphPar
summarize(OutputStream) - Method in class org.metaqtl.ChromCluster.ClusterGraph
SVDAlgorithm - Class in org.metaqtl.algo
  This class defines methods to solve usual linear algebra problems by using Singular Value Decomposition (SVD) strategy.
SVDAlgorithm() - Constructor for class org.metaqtl.algo.SVDAlgorithm
SVDBackSub(double[][], double[], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Solves A.X=B for a vector X, where `A` is specified by the matrix `U`,`V` and the vector `w` as returned by the SVDecomposition() method.
SVDecomposition(double[][], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Given a matrix `A`, this routine computes its singular value decomposition A = U.W.V' .
SVDMFit(double[][], double[], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Given a set of data points y[1..m] with indiviudal weights w[1..m], use chi2 minimization to determine the coefficients a[1..n] of the fitting function y = X*a.
swap - Variable in class org.metaqtl.Qtl.QTLProj
  True if the flanking marker order are inversed between the skeleton and the original map.
synchChromGraphs(ChromGraph[], Set) - Static method in class org.metaqtl.main.MetaMain
SYNONYMS - Static variable in interface org.thalia.bio.IOntologyTermProperties
  The synonyms property for a term in a ontology.

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